It has been demonstrated that when illuminated with light, metallic cavity arrays support extraordinary transmission with resonances at specific frequencies, which are strongly related to the cavity array periodicity. See T. W. Ebbesen, H. J. Lezec, H. F. Gaemi, T. Thio, and P. A. Wolff, “Extraordinary optical transmission through sub-wavelength cavity arrays,” Nature (London) 391, 667 (1998). Several models have been suggested to describe this phenomenon. See L. Martin-Moreno, F. J. Garcia-Vidal, H. J. Lezec, K. M. Pellerin, T. Thio, J. B. Pendry, and T. W. Ebbesen, “Theory of Extraordinary Optical Transmission through Subwavelength Cavity Arrays,” Phys. Rev. Lett. 86, 1114 (2001); C. Genet, M. P. van Exter, J. P. Woerdman, “Fano-type interpretation of red shifts and red tails in cavity array transmission spectra,” Opt. Commun. 225, 331 (2003); and H. J. Lezec, T. Thio, “Diffracted evanescent wave model for enhanced and suppressed optical transmission through subwavelength cavity arrays,” Opt. Exp. 12, 3629 (2004). Most of these invoke the role of surface plasmon polaritons (SPPs). SPPs are surface electromagnetic waves formed by collective oscillation of electrons at a metal-dielectric interface. See H. Raether, Surface Plasmons on Smooth and Rough Surfaces and on Gratings, (Springer-Verlag, Berlin, 1988). These models indicate that the extraordinary transmission occurs when the incident excitation matches the surface plasmon resonances. The light is strongly localized on subwavelength scales as plasmonic excitations and a resonance effect is accompanied by field enhancement.
One of the main possible areas of use for such metallic cavity arrays is in the microarray diagnostic technologies. The substrates generally used in a microarray platform consist of an array of microscopic spots of immobilized DNA oligonucleotides, peptides, or proteins. The complementary or desired sequence of another molecule, such as ssDNA attached or tagged with a fluorescent molecule (often with absorption maxima at 488 nm, 532 nm and 635 nm) hybridizes to complementary probes on the substrate. After the hybridization reaction these substrates are excited by laser sources corresponding to the fluorescent molecules used, and fluorescence intensity is read or scanned with a microarray scanner. The concentrations of DNA oligomers immobilized on such substrates are typically in the nanomolar to picomolar ranges. The metallic cavity arrays under illumination redistribute light inside the cavities through the excitation of surface plasmons thereby increasing the local intensity. By immobilizing the DNA oligonucleotides inside the cavities and using them as tiny reaction chambers for hybridization, it is possible to take advantage of the local intensity enhancements for improving the emitted fluorescence intensity. See M. J. Heller, “DNA microarray technologies: Devices, systems and applications,” Annu. Rev. Biomed. Eng., 4, 129 (2002); Y. Liu, F Mandavi, and S. Blair “Enhanced Fluorescence Transduction Properties of Metallic cavity Arrays,” IEEE J. Selected Topics in Quantum Electronic 11, 778 (2005); and S. Fore, Y, Yuen, L. Hesselink, T. Huser, “Pulsed-interleaved excitation FRET measurements on single duplex DNA molecules inside C-shaped cavities” Nano. Lett. 7 1749 (2007).
However, many conventional metallic cavity arrays are limited in the ability to control or tune the enhancement in light transmission through the cavities and/or light intensity within the cavities. As a result, the sensitivity, accuracy, and specificity of assays using such cavity arrays is limited.